Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA
Grazieli Maboni1,2#, Rodrigo de Paula Baptista3,4,5, Joy Wireman6, Isaac Framst2, Anne O. Summers6, Susan Sanchez1,7
Affiliations
1 Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, GA 30602, USA
2 Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
3 Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
4 Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
5 Department of Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
6 Department of Microbiology, University of Georgia, Athens, GA 30602, USA
7 Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
# Corresponding author: Grazieli Maboni, gmaboni@uoguelph.ca
Maboni, G.; Baptista, R.d.P.; Wireman, J.; Framst, I.; Summers, A.O.; Sanchez, S. Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA. Antibiotics 2022, 11, 1400. https://doi.org/10.3390/antibiotics11101400
This repository contains supporting documentation for hybrid Illumina miSeq and Oxford Nanopore minION bacterial plasmid assembly for the detection of antimicrobial susceptibility genotypes. Each pipeline serves as a wrapper for the pipeline components and corresponds to a unique combination of assembly methods and tools. Pipelines can be grouped into four main methods:
- Nanopore-only assembly
- Illimuna-only assembly
- Hybrid assembly (simultaneous assembly of Illumina reads and Nanopore reads)
- Nanopore-polished (Flye-assembled Nanopore reads post-hoc matched with Illumina reads)
Total genomic DNA
- Genomic Nanopore Flye (Nanopore-only assembly)
- Genomic Nanopore polished Flye (Nanopore-polished assembly, Flye-assembled Nanopore reads post-hoc matched with Illumina reads)
- Genomic Illumina (Illumina-only assembly)
- Genomic Hybrid (simultaneous assembly of Illumina reads and Nanopore reads)
Plasmid only DNA
- Plasmid Nanopore Flye (Nanopore-only assembly)
- Plasmid Nanopore Canu (Nanopore-only assembly)
- Plasmid Nanopore polished Flye (Nanopore-polished assembly, Flye-assembled Nanopore reads post-hoc matched with Illumina reads)
- Plasmid Nanopore polished Canu (Nanopore-polished assembly, Canu-assembled Nanopore reads post-hoc matched with Illumina reads)
- Plasmid Illumina (Illumina-only assembly)
- Plasmid Hybrid (simultaneous assembly of Illumina reads and Nanopore reads)
HybridAMR relies on the use of previously developed open-source software. The specific integration and configuraion of these tools is determined by the specific needs of each pipeline. This pipeline requires Linux or macOS; it is possible to use this pipeline with Apple Silicon Macs, either through Rosetta2 or by building the dependencies from source.
Install using command line with conda, homebrew, or build dependencies from source. Windows installation not currently supported.
Reccomended system requirements: 8 core CPU, 32gb system memory, 500gb SSD
Please see the install and usage document for details.